PadMetBio
STIC AMSUD
Parallel and Distributed Metaheuristics for Structural Bioinformatics
Structural bioinformatics deals with problems where the rules that govern the biochemical processes and relations are partially known which makes hard to design efficient computational strategies for these problems. There is a wide range of unanswered questions, which cannot be answered neither by experiments nor by classical modeling and simulation approaches. Specifically, there are several problems that still do not have a computational method that can guarantee a minimum quality of solution. The general goal of this project is to develop metaheuristics models based on robust and scalable parallel and distributed computing for structural bioinformatic problems. International Project (Stic-Amsud 2016) between the Federal University of Rio Grande do Sul (UFRGS, Brazil), University of Nacional de San Luis (UNSL, Argentine), University of Santiago de Chile (USACH, Chile), University of Pierre et Marie Currie (UPMC, LIP6, INRIA, France).
Researchers
- Dr. Rodrigo Ligabue Braun DF/UFCSPA
- Dr. Rodrigo Ligabue Braun DF/UFCSPA
- Dr. Hugo Verli PPGBCM/CBiot/UFRGS
- Dr. Erika Rosas DI/UTFSM
- Dr. Marcela Printista LIDIC/UNSL
- Dr. Sébastien Monnet LIP6/INRIA
- Dr. Julien Sopena LIP6/INRIA
- Dr. Pierre Sens LIP6/INRIA
Graduate Students/Collaborators
Study Missions
Work Missions
PROBRAL Meetings / Presentations
2017 - First Meeting
2017 - Second meeting
2018 - Third meeting
2018 - Fourth meeting
Publications
- Towards rapid population genetics forward-in-time simulations SEPULVEDA, V.; SOLAR, R.; INOSTROSA-PSIJAS, A.; GIL-COSTA, V.; MARIN, M. Proceedings of the 2017 Winter Simulation Conference (WSC '17), p. 1–12, 2017.
- A Service-Oriented Platform for Approximate Bayesian Computation in Population Genetics SOLAR, R.; SEPULVEDA, V.; INOSTROSA-PSIJAS, A.; ROJAS, O.; GIL-COSTA, V.; MARIN, M. Journal of Computational Biology, v. 26, p. 266-279, 2019.
- A Genetic Algorithm Based on Restricted Tournament Selection for the 3D-PSP Problem BORGUESAN, B.; NARLOCH, P. H.; INOSTROZA-PONTA, M.; DORN, M. 2018 IEEE Congress on Evolutionary Computation (CEC), 2018.
- Understanding the Relationship Between Decision and Objective Space in the Multi-Objective Phylogenetic Inference Problem VILLALOBOS-CID, M.; DORN, M.; INOSTROZA-PONTA, M. 2018 IEEE Congress on Evolutionary Computation (CEC), p. 1-8, 2018.
- Performance Comparison of Multi-Objective Local Search Strategies to Infer Phylogenetic Trees VILLALOBOS-CID, M.; DORN, M.; INOSTROZA-PONTA, M. 2018 IEEE Congress on Evolutionary Computation (CEC), p. 1-8, 2018.
- Using local search strategies to improve the performance of NSGA-II for the Multi-Criteria Minimum Spanning Tree problem PÁRRAGA-ÁLAVA, J.; DORN, M.; INOSTROZA-PONTA, M. 2017 IEEE Congress on Evolutionary Computation (CEC), p. 1-8, 2017.
- An evolutionary multi-agent algorithm to explore the high degree of selectivity in three-dimensional protein structures CORRÊA, L. L.; INOSTROZA-PONTA, M.; DORN, M. 2017 IEEE Congress on Evolutionary Computation (CEC), p. 1-8, 2017.
- A Memetic Algorithm for 3D Protein Structure Prediction Problem CORRÊA, L.; BORGUESAN, B.; FARFÁN, C.; INOSTROZA-PONTA, M.; DORN, M. IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 15, p. 690-704, 2018.
- A multi-objective gene clustering algorithm guided by apriori biological knowledge with intensification and diversification strategies PARRAGA-ALAVA, J.; DORN, M.; INOSTROZA-PONTA, M. BioData Mining, v. 11, p. 1-22, 2018.
- A Memetic Algorithm Based on an NSGA-II Scheme for Phylogenetic Tree Inference CID-VILLALOBOS, M.; DORN, M.; LIGABUE-BRAUN, R.; INOSTROZA-PONTA, M. IEEE Transactions on Evolutionary Computation, v. 23, p. 776-787, 2019.
- NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Protein BORGUESAN, B.; INOSTROZA-PONTA, M.; DORN, M. Journal of Computational Biology, v. 24, p. 255-265, 2017.